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Question: Using galaxy with Oracle database?
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gravatar for fiebig
2.6 years ago by
fiebig • 30
fiebig • 30 wrote:

Hello,

lately I tried to connect our local Galaxy instance to our Oracle 12c database. I managed to establish the connection and the first table "migrate_version" was created in the schema. Then the setup was canceled with the message, that the "table identifier is to long."

Indeed Oracle table names, column names ect. have a maximum length of 30 characters. Some of the Galaxy sqlite table names exceed that limit, example table: "cleanup_event_library_dataset_association" (41 characters).

Is there anybody who actively uses an Oracle DB together with Galaxy?!? Every hint/solution/howto is appreciated. At the moment I'm under the impression, that it is not possible to use Oracle DBs.

Greetings, Anne
galaxy oracle • 755 views
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modified 2.6 years ago by Bjoern Gruening ♦ 5.1k • written 2.6 years ago by fiebig • 30
0
gravatar for Jennifer Hillman Jackson
2.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello Anne,

I do not know of any groups using Oracle with Galaxy. The recommended database choices are included here, Section 3.2: https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer

Others that have used Oracle with Galaxy successfully are welcome to post!

Best, Jen, Galaxy team
ADD COMMENT • link written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for Bjoern Gruening
2.6 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

Not really related but an interesting read: http://stackoverflow.com/questions/1378133/why-are-oracle-table-column-index-names-limited-to-30-characters

If you can stay away from Oracle ;)
ADD COMMENT • link written 2.6 years ago by Bjoern Gruening ♦ 5.1k

hmm, somehow I expected this answer. Integrating the Galaxy DB in the institutes main DB, curated by an DBA would have been very comfortable. Oracle rules are sometimes a bit creepy (MVs)...ok, I'm going to inform about Postgresql.

ADD REPLY • link written 2.6 years ago by fiebig • 30
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